Krochmal D, Roman C, Lewicka A, Shao Y, Piccirilli JA, Structural basis for promiscuity in ligand recognition by yjdF riboswitch, Cell Discov. 2024


Weissman B, Ekesan S, Lin HC, Gardezi S, Li NS, Giese TJ, McCarthy E, Harris ME, York DM, Piccirilli JA, A dissociative transition state in Hepatitis Delta Virus ribozyme catalysis, J. Am. Chem. Soc. 2023

Li NS, Piccirilli JA, Greene GL, Demethylation of Dimethyl Phosphonate Esters with Sodium Ethanethiolate: Improved Synthesis of 5´-Methylene Substituted 2´,5´-Deoxyribonucleotides” Nucleosides, Nucleotides & Nucleic Acids 2023

Lewicka A, Roman C, Jones S, Disare M, Rice PA, Piccirilli JA, Crystal structure of a cap-independent translation enhancer RNA. Nucleic Acids Res. 2023

Li NS, Piccirilli JA, Greene GL, Reinvestigating the Synthesis and Characterization of Ethyl 3-[5-(2-Ethoxycarbonyl-1-methylvinyloxy)-1-methyl-1H-indol-3-yl]-but-2-enoate. ACS Omega. 2023

Yoon S, Ollie E, York DM, Piccirilli JA, Harris ME, Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis. Biochemistry. 2023

Li NS, Dai Q, Weissman B, Harris ME, Piccirilli JA, A general and efficient approach to synthesize the phosphoramidites of 5′-18O labeled purine nucleosides. Nucleosides Nucleotides Nucleic Acids. 2023


Krochmal D, Shao Y, Li NS, DasGupta S, Shelke SA, Koirala D, Piccirilli JA, Structural basis for substrate binding and catalysis by a self-alkylating ribozyme, Nat. Chem. Biol. 2022

Rees HC, Gogacz W, Li NS, Koirala D, Piccirilli JA, Structural basis for fluorescence activation by Pepper RNA, ACS Chem. Biol. 2022

Liu D, Thélot FA, Piccirilli JA, Liao M, Yin P, Sub-3-Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly. Nat Methods. 2022


Ganguly A, Weissman BP, Giese TJ, Li NS,  Hoshika S, Rao S, Benner SA, Piccirilli JA, York DM, Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme, Nat Chem. 2021

DasGupta S, Piccirilli JA, The Varkud Satellite Ribozyme: A Thirty-Year Journey through Biochemistry, Crystallography, and Computation, Acc Chem Res. 2021

DasGupta S, Nykiel K, Piccirilli JA, The hammerhead self-cleaving motif as a precursor to complex endonucleolytic ribozymes, RNA. 2021

Roman C, Lewicka A, Koirala D, Li NS, Piccirilli JA, The SARS-CoV‑2 Programmed −1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 Å Using Chaperone-Assisted RNA
Crystallography. ACS Chem. Biol. 2021

Li NS, Koo SC, Piccirilli JA, Synthesis of oligoribonucleotides containing a 2´-amino-5´-S-phosphorothiolate linkage, J. Org. Chem. 2021

Liu D, Shao Y, Piccirilli JA, Weizmann Y, Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution. Sci Adv. 2021


Gaines CS, Piccirilli JA, York DM, The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design, RNA. 2020

Liu D, Geary CW, Chen G, Shao Y, Li M, Mao C, Andersen ES, Piccirilli JA, Rothemund PWK, Weizmann Y, Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures, Nat Chem. 2020

Hiller DA, Dunican BF, Nallur S, Li NS, Piccirilli JA, Strobel SA, The Positively Charged Active Site of the Bacterial Toxin RelE Causes a Large Shift in the General Base pKa, Biochemistry 2020

Koirala D, Lewicka A, Koldobskaya Y, Huang H, Piccirilli JA. Synthetic Antibody Binding to a Preorganized RNA Domain of Hepatitis C Virus Internal Ribosome Entry Site Inhibits Translation. ACS Chem. Biol. 2020


Ganguly A, Weissman BP, Piccirilli JA, York DM, Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme,
ACS Catal. 2019

Li NS, Liang W, Piccirilli JA, Tang WJ. Reinvestigating the synthesis and efficacy of small benzimidazole derivatives as presequence protease enhancers. Eur J Med Chem. 2019

Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AW, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA. A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nat. Commun. 2019

Bevilacqua PC, Harris ME, Piccirilli JA, Gaines C, Ganguly A, Kostenbader K, Ekesan Ş, York DM. An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes. ACS Chem Bio 2019.

Wilson TJ, Liu Y, Li NS, Dai Q, Piccirilli JA, Lilley DMJ. Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes. JACS 2019.

Hoshika S, Leal NA, Kim M, Kim M, Karalkar NB, Kim H, Bates AM, Watkins NE, SantaLucia HA, Meyer AJ, DasGupta S,  Piccirilli JA, Ellington AD, SantaLucia J, Georgiadis MM, Benner SA. Hachimoji DNA and RNA: A genetic system with eight building blocks. Science 2019.


Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA,  Piccirilli JA. Structural basis for activation of fluoregenic dyes by an RNA aptamer lacking a G-quadruplex motif. Nat. Commun. 2018.

Lu J, Koo SC, Weissman B, Harris ME, Li NS,  Piccirilli JA. Evidence that nucleophile deprotonation exceeds bond formation in the HDV ribozyme transition state. Biochemistry 2018.

Koirala D, Shelke, SA, Dupont, M, Ruiz, S, DasGupta S, Bailey, LJ, Benner, SA,  Piccirilli JA. Affinity maturation of a portable Fab-RNA module for Chaperone-assisted RNA crystallography.  Nucleic Acids Res. 2018.


Li NS, Lu, J, Piccirilli JA. Synthesis of 5′-Thio-3′-O-Ribonucleoside Phosphoramidites. J. Org. Chem. 2017.

Harris ME, York DM, Piccirilli JA, Anderson VE. Kinetic Isotope Effect analysis of RNA 2′-O-Transphosphorylation. Methods Enzymol. 2017.

DasGupta S, Suslov NB, Piccirilli JA. Structural basis for substrate helix remodeling and cleavage loop activation in the Varkud satellite ribozyme. JACS. 2017 

Liu D, Shao Y, Chen G, Tse-Dinh, Y-C,  Piccirilli JA, Weizmann, Y. Synthesizing topological structures containing RNA.  Nat. Commun. 2017.

Sundaram KM, Zhang Y, Mitra AK, Kouadio, JK, Gwin K, Roman BR, Kossiakoff AA, Lengyel E, Piccirilli JA. Prolactin receptor-mediated internalization of imaging agents detects epithelial ovarian cancer with enhanced sensitivity and specificity. Cancer Res. 2017 Feb 15.

Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki J, Chen SJ, Cheng CY, Chou FC, Ferré-D’Amaré AR, Das R, Dawson WK, Feng D, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ,  Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J Jr, Sarzynska J, Szachniuk M, Tandon A, Traus. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA. 2017 Jan 30.


Biondi E, Lane JD, Das D, DasGupta S,  Piccirilli JA, Hoshika S, Bradley KM, Krantz BA, Benner SA. Lanoratory evolution of artificially expanded DNA gives redesignable aptamer that target the toxic form of anthrax protective antigen. Nucleic Acids Res. 2016 Oct 3.

Li NS, Gossai N, Naumann JA, Gordon PM,  Piccirillli JA. Efficient Synthetic Approach to Linear Dasatanib-DNA Conjugates by Click Chemistry. Bioconjugate Chem 2016 Sep 30.

Shao Y*, Huang H*, Qin D, Li NS, Koide A, Staley JP, Koide S, Kossiakoff AA,  Piccirilli JA. Specific Recognition of a Single-stranded RNA Sequence by a Synthetic Antibody Fragment. (*Equal Contribution)  J Mol Biol. 2016 Sep 2.

Piccirilli JA, Staley JP. Reverse transcriptases lend a hand in splicing catalysis. Nat Struct Mol Biol. 2016 Jun 7;23(6):507-9

Gossai NP, Naumann JA, Li NS, Zamora EA, Gordon DJ,  Piccirilli JA, Gordon PM. Drug conjugated nanoparticles activated by cancer cell specific mRNA. Oncotarget. 2016 May 18.

Zhang S, Gu H, Chen H, Strong E, Ollie EW, Kellerman D, Liang D, Miyagi M, Anderson VE, Piccirilli JA, York DM, Harris ME. Isotope effect analyses provide evidence for an altered transition state for RNA 2’O-transphosphorylation catalyzed by Zn2+. Chem Commun. 2016. Feb 9. 

Roy S, Ly D, Castro CD, Li NS, Hawk AJ, Altman JD, Meredith SC,  Piccirilli JA, Moody DB, Adams EJ. Molecular Analysis of Lipid-Reactive Vδ1 γδ T Cells Identified by CD1c Tetramers. J Immunol. 2016 Jan 11. pii.

Sengupta RN, van Schie SN, Giambaşu G, Dai Q, Yesselman JD, York D, Piccirilli JA, Herschlag D. An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions. RNA. 2016 Jan;22(1):32-48


Suslov NB*, DasGupta S*, Huang H, Fuller JR, Lilley DM, Rice PA,  Piccirilli JA. Crystal structure of the Varkud satellite ribozyme. (*Equal Contribution) Nat. Chem. Biol. 2015 11, 840-846.

Anderson VE,  Piccirilli JA, Fitzpatrick PF, Marlier JF, Hengge AC, Byers LD, Wong KY, York DM, Harris ME. Enzyme Transition States from Theory and Experiment. Biochim Biophys Acta. 2015 Aug 21. S1570-9639(15)00220-4.

Hernandez AR *, Shao Y*, Hoshika S*, Yang Z, Shelke SA, Herrou J, Kim H-J,  Kim MJ, Piccirilli JA, Benner SA. A Crystal structure of a Functional RNA Molecule Containing an Artificial Nucelobase Pair. (*Equal Contribution) Angew. Chemieearly view.

Koo SC, Lu J, Li NS, Leung E, Das SR, Harris ME,  Piccirilli JA.  Transition State Features in the Hepatitis Delta Virus (HDV) Ribozyme Reaction Revealed by Atomic Perturbations. JACSjust accepted.

DasGupta S, Shelke SA, Li NS,  Piccirilli JA. Spinach RNA aptamer detects lead(II) with high selectivity.  Chem Commun (Camb). 2015 May 5.

Kellerman DL, Simmons KS, Pedraza M,  Piccirilli JA, York DM, Harris ME. Determination of HDV ribozyme N(-1) nucleobase and functional group specificity using internal competition kinetics. Anal Biochem. 2015 May 1. pii: S0003-2697(15)00201-8.

Harris ME,  Piccirilli JA, York DM. Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism. Biochim Biophys Acta. 2015 Apr 29. pii: S1570-9639(15)00131-4.

Weissman BP, Li NS, York D, Harris M,  Piccirilli JA.  Heavy Atom Labeled Nucleotides for Measurement of Kinetic Isotope Effects. Biochim Biophys Acta. 2015 Mar 27.

Chen H,  Piccirilli JA, Harris ME, York DM. Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2′-O-transphosphorylation interpreted through kinetic isotope effects. Biochim Biophys Acta. 2015 Mar 23.

Lu J, Koo SC, Li NS and  Piccirilli JA. Synthesis of 2′-O-photocaged ribonuleoside phosphoramidites. Nucleosides, Nucleotides and Nucleic Acids. 2015 34(2), 114-129.


Shelke SA,  Piccirilli JA. Origins of life: RNA made in its own mirror image. Nature. 2014 Oct 29.

Roy S, Ly D, Li NS, Altman JD,  Piccirilli JA, Moody DB, Adams EJ. Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by αβ T cells. Proc Natl Acad Sci U S A. 2014 Oct 8.

Kellerman DL, York DM,  Piccirilli JA, Harris ME. Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2′-O-transphosphorylation. Curr Opin Chem Biol. 2014 Jul 11;21C:96-102.

Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA,  Piccirilli JA.  A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Nat Chem Biol. 2014 Jun 22.

Fica SM, Mefford MA, Piccirilli JA, Staley JP. Evidence for a group II intron-like catalytic triplex in the spliceosome.   Nat Struct Mol Biol. 2014 Apr 20. doi: 10.1038/nsmb.2815.

Li NS, Tuttle N, Staley JP,  Piccirilli JA. Synthesis and Incorporation of the Phosphoramidite Derivative of 2′-O-Photocaged 3′-S-Thioguanosine into Oligoribonucleotides: Substrate for Probing the Mechanism of RNA Catalysis.   J Org Chem. 2014 Mar 17. [Epub ahead of print]


Li NS, Piccirilli JA. Synthesis of stereopure acyclic 1,5-dimethylalkane chirons: building blocks of highly methyl-branched natural products. Tetrahedron. 2013 Nov 18;69(46);9633-9641

Fica SM *, Tuttle N*, Novak T, Li NS, Lu J, Koodathingal P, Dai Q, Staley JP, Piccirilli JA. RNA catalyses nuclear pre-mRNA splicing. (*Equal Contribution)  Nature. 2013 Nov 14;503(7475):229-34.

Keenholtz RA, Mouw KW, Boocock MR, Li NS,  Piccirilli JA, Rice PA.  Arginine as a General Acid Catalyst in Serine Recombinase-mediated DNA Cleavage. J Biol Chem. 2013 Oct 4;288(40):29206-29214.

Gu H, Zhang S, Wong KY, Radak BK, Dissanayake T, Kellerman DL, Dai Q, Miyagi M, Anderson VE, York DM,  Piccirilli JA, Harris ME.  Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2′-O-transphosphorylation. Proc Natl Acad Sci U S A. 2013 Aug 6;110(32):13002-7.

Li NS, Scharf L, Adams EJ, Piccirilli JA. Highly stereocontrolled total synthesis of β-D-mannosyl phosphomycoketide: a natural product from Mycobacterium tuberculosis.     J Org Chem. 2013 Jun 21;78(12) :5970-86.

Hernandez AR, Piccirilli JA. Chemical  origins of life: Prebiotic RNA unstuck. Nat Chem. 2013 May;5(5):360-2.


Li NS, Frederiksen JK, Piccirilli JA. Automated Solid-Phase Synthesis of RNA Oligonucleotides Containing a Nonbridging Phosphorodithioate Linkage via Phosphorothioamidites. J Org Chem. 2012 Nov 2;77(21):9889-92

Kath-Schorr S, Wilson TJ, Li NS, Lu J, Piccirilli JA, Lilley DM. General acid-base catalysis mediated by nucleobases in the hairpin ribozyme.  J Am Chem Soc. 2012 Sep 7.

Sakaguchi, R., Giessing, A., Dai, Q., Lahoud, G., Liutkeviciute, Z., Klimasauskas, S., Piccirilli, J., Kirpekar, F. & Hou, Y. M. (2012). Recognition of guanosine by dissimilar tRNA methyltransferases. RNA 18, 1687-701.

Li NS, Piccirilli JA. Efficient synthesis of 2′-C-α-aminomethyl-2′-deoxynucleosides.  Chem Commun 2012 Sep 11;48(70):8754-6.

Frederiksen JK, Li NS, Das R, Herschlag D, Piccirilli JA. Metal-ion rescue revisited: Biochemical detection of site-bound metal ions important for RNA folding.  RNA. 2012 Apr 26.

Sengupta RN, Herschlag D, Piccirilli JA. Thermodynamic Evidence for Negative Charge Stabilization by a Catalytic Metal Ion within an RNA Active Site.  ACS Chem Biol. 2012 Feb 17;7(2):294-9.

Wong KY, Gu H, Zhang S, Piccirilli JA, Harris ME, York DM. Characterization of the reaction path and transition States for RNA transphosphorylation models from theory and experiment. Angew Chem Int Ed Engl.  2012 Jan 16;51(3):647-51.


Dai Q, Sengupta R, Deb SK, Piccirilli JA. Synthesis of 2′-N-Methylamino-2′-deoxyguanosine and 2′-N,N-Dimethylamino-2′-deoxyguanosine and Their Incorporation into RNA by Phosphoramidite Chemistry. J Org Chem. 2011 Nov 4;76(21):8718-25.

Piccirilli JA, Koldobskaya Y.  Crystal structure of an RNA polymerase ribozyme in complex with an antibody fragment. Philos Trans R Soc Lond B Biol Sci. 2011 Oct 27;366(1580):2918-28.

Li NS, Frederiksen JK, Piccirilli JA. Synthesis, Properties, and  Applications of Oligonucleotides Containing an RNA Dinucleotide Phosphorothiolate Linkage. Acc Chem Res. 2011 Dec 20;44(12):1257-69.

Leung EK, Suslov N, Tuttle N, Sengupta R, Piccirilli JA. The Mechanism of Peptidyl Transfer Catalysis by the Ribosome. Annu Rev Biochem. 2010 Jun 23.  Annu Rev Biochem. 2011 Jun 7;80:527-55.

Forconi M, Porecha RH, Piccirilli JA, Herschlag D. Tightening of Active Site Interactions En Route to the Transition State Revealed by Single-Atom Substitution in the Guanosine-Binding Site of the Tetrahymena Group I Ribozyme.
J Am Chem Soc. 2011 May 25;133(20):7791-800.

Gilbreth RN, Truong K, Madu I, Koide A, Wojcik JB, Li NS, Piccirilli JA, Chen Y, Koide S. Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design.  Proc Natl Acad Sci U S A. 2011, 108, 7751-7756.

Plantinga MJ, Korennykh AV, Piccirilli JA, Correll CC. The ribotoxin restrictocin recognizes its RNA substrate by selective engagement of active site residues.  Biochemistry. 2011 Apr 12;50(14):3004-13.

Ramu, H., Vazquez-Laslop, N., Klepacki, D., Dai, Q., Piccirilli, J., Micura, R., Mankin, A.S. Nascent Peptide in the Ribosome Exit Tunnel Affects Functional Properties of the A-Site of the Peptidyl Transferase Center.  Mol Cell. 2011, 41, 321-330.

Koldobskaya Y, Duguid EM, Shechner DM, Suslov NB, Ye J, Sidhu SS, Bartel DP, Koide S, Kossiakoff AA, Piccirilli JA. A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination.  Nat Struct Mol Biol. 2011 Jan;18(1):100-6.

Li NS, Frederiksen JK, Koo SC, Lu J, Wilson TJ, Lilley DM, Piccirilli JA.  A general and efficient approach for the construction of RNA oligonucleotides containing a 5′-phosphorothiolate linkage.   Nucleic Acids Res. 2011 Mar;39(5):e31.

Forconi M, Schwans JP, Porecha RH, Sengupta RN, Piccirilli JA, Herschlag D. 2′-Fluoro substituents can mimic native 2′-hydroxyls within structured RNA.  Chem Biol. 2011 Aug 26;18(8):949-54.


Scharf L, Li NS, Hawk AJ, Garzón D, Zhang T, Fox LM, Kazen AR, Shah S, Haddadian EJ, Gumperz JE, Saghatelian A, Faraldo-Gómez JD, Meredith SC, Piccirilli JA, Adams EJ. The 2.5 å structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation. Immunity. 2010 Dec 14;33(6):853-62.

Mouw KW, Steiner AM, Ghirlando R, Li NS, Rowland SJ, Boocock MR, Stark WM, Piccirilli JA, Rice PA. Sin Resolvase Catalytic Activity and Oligomerization State are Tightly Coupled.  J Mol Biol. 2010 Nov 19;404(1):16-33.

Koodathingal P, Novak T, Piccirilli JA, Staley JP. The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5′ splice site cleavage during pre-mRNA splicing.  Mol Cell. 2010 Aug 13;39(3):385-95.

Harris ME, Dai Q, Gu H, Kellerman DL, Piccirilli JA, Anderson VE. Kinetic isotope effects for RNA cleavage by 2′-O- transphosphorylation: nucleophilic activation by specific base.  J Am Chem Soc. 2010 Aug 25;132(33):11613-21.

Lu J, Li N-S, Koo, SC, Piccirilli JA. Efficient synthesis of N4-methyl- and N5-hydroxycytidine phosphoramidites. Synthesis 2010 2708-2712.

Li N-S, Lu J, Piccirilli JA. Synthesis of 2′-C-branched nucleosides. Organic Preparations and Procedures International 2010 42:191-283.

Wilson TJ, Li NS, Lu J, Frederiksen JK, Piccirilli JA, Lilley DM. Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme.  Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):11751-6.

Forconi M, Sengupta RN, Piccirilli JA, Herschlag D. A rearrangement of the guanosine-binding site establishes an extended network of functional interactions in the Tetrahymena group I ribozyme active site.  Biochemistry. 2010 Mar 30;49(12):2753-62.


Shechner DM, Grant RA, Bagby SC, Koldobskaya Y, Piccirilli JA, Bartel DP. Crystal structure of the catalytic core of an RNA-polymerase ribozyme.  Science. 2009 Nov 27;326(5957):1271-5.

Lu J., Li N-S., Koo S.C., Piccirilli J.A. Synthesis of Pyridine, Pyrimidine and Pyridinone C-Nucleoside Phosphoramidites for Probing Cytosine Function in RNA.  J Org Chem. 2009 Nov 6;74(21):8021-30.

Forconi M., Sengupta R.N., Liu M.C., Sartorelli A.C., Piccirilli J.A., Herschlag D. Structure and function converge to identify a hydrogen bond in a group I ribozyme active site.  Angew Chem Int Ed Engl. 48:7171-5 (2009).

Frederiksen J.K., Piccirilli JA. Identification of catalytic metal ion ligands in ribozymes.  Methods, 49:148-66 (2009).

Dai Q, Saikia, M, Li N-S., Pan T., and Piccirilli J.A. Efficient chemical synthesis of AppDNA by adenylation of immobilized DNA-5-monophosphate.  Org. Lett., 11:1067-1070 (2009).

Li, N-S., Lu, J., and Piccirilli, J.A. Synthesis of 2-C–methyl-2deoxyguanosine.  J. Org. Chem., 74:2227-2230 (2009).


Plantinga, M.J., Korennykh, A.V., Piccirilli, J.A., and Correll, C.C. Electrostatic interactions guide the active site face of a structure-specific ribonuclease to its RNA substrate.  Biochemistry, 47:8912-18 (2008).

Forconi, M., Lee, J., Lee, J., Piccirilli, J.A., and Herschlag, D. Functional identification of ligands for a catalytic metal ion in Group I introns.  Biochemistry, 47:6883-94 (2008).

Hougland, J.L., Sengupta, R.N., Qing, D., Deb, S.K., and Piccirilli, J.A. The 2-hydroxyl group of the guanosine nucleophile donates a functionally important hydrogen bond in the Tetrahymena ribozyme reaction.  Biochemistry, 47:7684-94 (2008).

Lu, J., Li, N-S., Sengupta, R., and Piccirilli, J.A. Synthesis and biochemical application of 2′-O-methyl-3′-thioguanosine as a probe to explore group I intron catalysis  Bioorganic & Medicinal Chemistry, 16:5754-60 (2008).

Das, R., Kudaravalli, M., Jonikas, M., Laederach, A., Fong, R., Schwans, J. P., Baker, D., Piccirilli, J. A., Altman, R. B., and Herschlag, D. (2008) Structural inference of native and partially folded RNA by high-throughput contact mapping.  Proc Natl Acad Sci U S A 105:4144-9 (2008).

Dai, Q., Frederiksen, J. K., Anderson, V. E., Harris, M. E., and Piccirilli, J. A. Efficient synthesis of [2′-18O]uridine and its incorporation into oligonucleotides: a new tool for mechanistic study of nucleotidyl transfer reactions by isotope effect analysis.  J Org Chem 73:309-11 (2008).

Ye, J-D., Tereshko, V., Frederiksen, J.K., Koide, A., Fellouse, F.A., Sidhu, S.S., Koide, S., Kossiakoff, A.A., and Piccirilli, J.A. Synthetic antibodies for specific recognition and crystallization of structured RNA.  Proc Natl Acad Sci U S A 105:82-87 (2008).


Korennykh, A. V., Plantinga, M. J., Correll, C. C., and Piccirilli, J. A. Linkage between Substrate Recognition and Catalysis during Cleavage of Sarcin/Ricin Loop RNA by Restrictocin. Biochemistry, 46: 12744-12756 (2007).

Dai, Q., Fong, R., Saikia, M., Stephenson, D., Yu, Y. T., Pan, T., and Piccirilli, J. A. Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine.  Nucleic Acids Res., 35:6322-6329 (2007).

Ye, J. D., Li, N. S., Dai, Q., and Piccirilli, J. A. The mechanism of RNA strand scission: an experimental measure of the Bronsted coefficient, beta nuc.  Angew Chem Int Ed Engl 46:3714-7 (2007).

Korennykh, A. V., Correll, C. C., and Piccirilli, J. A. (2007) Evidence for the importance of electrostatics in the function of two distinct families of ribosome inactivating toxins.  RNA 13:1391-1396 (2007).

Forconi, M., Piccirilli, J. A., and Herschlag, D. Modulation of individual steps in group I intron catalysis by a peripheral metal ion.  RNA 13:1656-1667 (2007).

Li, N.-S., and Piccirilli, J. A. Synthesis of 2′-C-alpha-(Hydroxyalkyl) and 2′-C-alpha-Alkylcytidine Phosphoramidites: Analogues for Probing Solvent Interactions with RNA.  J Org Chem 72:1198-1210 .

Gordon, P. M., Fong, R., and Piccirilli, J. A. A Second Divalent Metal Ion in the Group II Intron Reaction Center.  Chem Biol 14:607-612 (2007).

Li, N.-S., Lu, J., and Piccirilli, J. A. Efficient synthesis of methyl 3,5-di-O-benzyl-alpha-D-ribofuranoside and application to the synthesis of 2′-C-beta-alkoxymethyluridines. Org. Lett. 9:3009-3012.  Org Lett 9:3009-3012 (2007).

Dai, Q., Lea, C. R., Lu, J., and Piccirilli, J. A. Syntheses of (2′)3′-15N-Amino-(2′)3′-deoxyguanosine and Determination of Their pKa Values by 15N NMR Spectroscopy.  Org Lett 9:3057-3060 (2007).

Ye, J.-D., Barth, C. D., Anjaneyulu, P. S. R., Tuschl, T., and Piccirilli, J. A. Reactions of phosphate and phosphorothiolate diesters with nucleophiles: comparison of transition state structures.  Org & Bio Chemistry 5:2491-2497 (2007).

Li, N-S. and Piccirilli, J.A. Synthesis of 2´-C–(Hydroxyalkyl) and 2´-C–Alkylcytidine Phosphoramidites: Analogues for Probing Solvent Interactions with RNA.  J. Org. Chem., 72:1198-1210 (2007).


Saikia, M., Dai, Q., Decatur, W.A., Fournier, M.J., Piccirilli, J.A., and Pan, T. A systematic, ligation-based approach to study RNA modifications.  RNA 12:1-9 (2006).

Li, N-S. and Piccirilli, J.A. Efficient Synthesis of 2′-C–methylguanosine.  J. Org. Chem. 71:4018-4020 (2006).

Korennykh, A.V., Piccirilli, J.A., and Correll, C.C. The electrostatic character of the ribosome surface enables extraordinarily rapid target location by ribotoxins.  Nat. Struct. & Mol. Biol., 13:3436-446 (2006).

Dai, Q., Deb, S.K., Hougland, J.L. and Piccirilli, J.A. Improved synthesis of 2′-amino-2′-deoxyguanosine and its phosphoramidite.  Biorg. & Med. Chem., 14:705-713 (2006).


Das, S. R., and Piccirilli, J.A. General acid catalysis by the hepatitis delta virus ribozyme. Nat. Chem. Biol., 1:45-52 (2005)

Hougland, J. L., Kravchuk, A.V., Herschlag, D., and Piccirilli, J.A. Functional identification of catalytic metal ion binding sites within RNA.  PLoS Biol.,3:1536-1548 (2005).

Ye, J-D., Liao, X., and Piccirilli, J. A. Synthesis of 2′-C-difluoromethyl-ribonucleosides and their enzymatic incorporation into oligonucleotides.  J. Org. Chem.,70:7902-7910 (2005).

Li, N-S. and Piccirilli, J.A. Synthesis of 2′-Deoxy-2′-C–methylpurine nucleosides. Synthesis, 17: 2865-2870 (2005).


Gordon PM, Fong R, Deb SK, Li NS, Schwans JP, Ye JD, Piccirilli JA. New Strategies for Exploring RNA’s 2′-OH expose the importance of solvent during group II intron catalysis.  Chem Biol. 2004 Feb;11(2):237-46.

Schwans JP, Li NS, Piccirilli JA. A Packing Density Metric for Exploring the Interior of Folded RNA Molecules.  Angew Chem Int Ed Engl. 2004 Jun 7;43(23):3033-7.

Li NS, Piccirilli JA. Synthesis of the phosphoramidite derivatives of 2′-deoxy-2′-C-alpha-methylcytidine and 2′-deoxy-2′-C-alpha-hydroxymethylcytidine: analogues for chemical dissection of RNA’s 2′-hydroxyl group.  J Org Chem. 2004 Jul 9;69(14):4751-9.

Dai Q, Piccirilli JA. Efficient Synthesis of 2′,3′-Dideoxy-2′-Amino-3′-Thiouridine.  Org Lett. 2004 Jun 24;6(13):2169-72.

Hougland JL, Deb SK, Maric D, Piccirilli JA. An atomic mutation cycle for exploring RNA’s 2-hydroxyl group.  J Am Chem Soc. 2004 Oct 27;126(42):13578-9.


Dai Q, Piccirilli JA. Synthesis of 2′-C-beta-fluoromethyluridine.  Org Lett. 2003 Mar 20;5(6):807-10.

Li NS, Piccirilli JA. Synthesis of the Phosphoramidite Derivative of 2 Deoxy-2-C–methylcytidine.  J Org Chem. 2003 Aug 22;68(17):6799-802.

Schwans JP, Cortez CN, Olvera JM, Piccirilli JA. 2′-Mercaptonucleotide Interference Reveals Regions of close Packing Within Folded RNA Molecules.  J Am Chem Soc. 2003 Aug 20;125(33):10012-8.


Szewczak AA, Kosek AB, Piccirilli JA, Strobel SA. Identification of an active site ligand for a group I ribozyme catalytic metal ion.  Biochemistry. 2002 Feb 26;41(8):2516-25.


Li NS, Tang XQ, Piccirilli JA. 2-C-branched ribonucleosides. 2. Synthesis of 2-C–trifluoromethyl pyrimidine ribonucleosides.  Org Lett. 2001 Apr 5;3(7):1025-8.

Shan S, Kravchuk AV, Piccirilli JA, Herschlag D. Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction.  Biochemistry. 2001 May 1;40(17):5161-71.

Liao X, Anjaneyulu PS, Curley JF, Hsu M, Boehringer M, Caruthers MH, Piccirilli JA. The Tetrahymena Ribozyme Cleaves a 5′-Methylene Phosphonate Monoester ~10²-Fold Faster than a Normal Phosphate Diester: Implications for Enzyme Catalysis of Phosphoryl Transfer Reactions.  Biochemistry. 2001 Sep 18;40(37):10911-26.

Gordon PM, Piccirilli JA. Metal ion coordination by the AGC triad in domain 5 contributes to group II intron catalysis.  Nat Struct Biol. 2001 Oct;8(10):893-8.

Kuo LY, Piccirilli JA. Leaving Group Stabilization by Metal Ion Coordination and Hydrogen Bond Donation is an Evolutionarily Conserved Feature of Group I Introns.  Biochim Biophys Acta. 2001 Dec 30;1522(3):158-66.


Yoshida A, Shan So, Herschlag D, Piccirilli JA. The Role of the Cleavage Site 2′-Hydroxyl in the Tetrahymena Group I Ribozyme Reaction.  Chem Biol. 2000 Feb;7(2):85-96.

Gordon PM, Sontheimer EJ, Piccirilli JA. Metal Ion Catalysis During the Exon-Ligation Step of Nuclear pre-mRNA splicing: Extending the Parallels Between the Spliceosome and Group II Introns.  RNA. 2000 Feb;6(2):199-205.

Hamm, M.L., Schwans, J. P. and Piccirilli, J.A. The Hammerhead Ribozyme Catalyzes the Deglycosylation of 2′-Mercaptocytidine. J. Am. Chem. Soc., 122:4223-4224 (2000)

Gordon PM, Sontheimer EJ, Piccirilli JA. Kinetic characterization of the second step of group II intron splicing: Role of metal ions and the cleavage site 2′-OH in catalysis.  Biochemistry. 2000 Oct 24;39(42):12939-52.

Hamm, M.L., Nikolic, D., van Breemen, R.B., and Piccirilli, J.A. Unconventional origin of metal ion rescue in the hammerhead ribozyme reaction: Mn2+ -assisted redox conversion if 2-mercaptocytidine to cytidine. J. Am. Chem. Soc. 122:12069-12078, (2000).

Warnecke JM, Sontheimer EJ, Piccirilli JA, Hartmann RK. Active site constraints in the hydrolysis reaction catalyzed by bacterial RNase P: analysis of precursor tRNAs with a single 3′-S-phosphorothiolate internucleotide linkage.  Nucleic Acids Res. 2000 Feb 1;28(3):720-7.

Earnshaw DJ, Hamm ML, Piccirilli JA, Karpeisky A, Beigelman L, Ross BS, Manoharan M, Gait MJ. nvestigation of the proposed interdomain ribose zipper in hairpin ribozyme cleavage using 2′-modified nucleosides.  Biochemistry. 2000 May 30;39(21):6410-21.


Brautigam, C.A., Sun, S., Piccirilli, J.A. and Steitz, T.A. Structures of Normal Single-Stranded DNA and Deoxyribo-3′-S-phosphorothiolates Bound to the 3′-5′ Exonucleolytic Active Site of DNA Polymerase I from Escherichia coli.  Biochemistry, 38:696-704 (1999).

Tang, X.-Q., Liao, X. and Piccirilli, J.A. 2′-C-Branched Ribonucleosides: Synthesis of the Phosphoramidite Derivatives of 2′-C-ß-Methylcytidine and Their Incorporation into Oligonucleotides.  J. Org. Chem., 64:747-754 (1999).

Yoshida, A., Sun, S. and Piccirilli, J. A. A New Metal Ion Interaction in the Tetrahymena Ribozyme Reaction Revealed by Double Sulfur Substitution.  Nat Struct Biol. 1999 Apr;6(4):318-21.

Piccirilli, J.A. Do Enzymes Obey the Baldwin Rules? A Mechanistic Imperative in Enzymatic Cyclization Reactions?  Chem Biol. 1999 Mar;6(3):R59-64.

Hamm, M.L. and Piccirilli, J.A. The Synthesis and Characterization of Oligonucleotides Containing 2′-S, 3′-O-Cyclic Phosphorothiolate Termini.  J Org Chem. 1999 Jul 23;64(15):5700-5704.

Sontheimer, E.J., Gordon, P.M. and Piccirilli, J.A. Metal Ion Catalysis During Group II Intron Self Splicing: Parallels with the Spliceosome.  Genes Dev. 1999 Jul 1;13(13):1729-41.

Shan, S., Yoshida, A., Sun, S., Piccirilli, J.A. and Herschlag, D. Three metal Ions at the active site of the Tetrahymena group I ribozyme.  Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12299-304.



Hamm, M. and Piccirilli, J.A. Incorporation of 2′ -Mercaptocytidine into Oligonucleotides via Phosphoramidite Chemistry.  J Org Chem. 1997 May 16;62(10):3415-3420.

Sontheimer, E. J., Sun, S. and Piccirilli, J. A. Metal Ion Catalysis During Premessenger RNA Splicing.  Nature. 1997 Aug 21;388(6644):801-5.

Sun, S., Yoshida, A. and Piccirilli, J. A. Synthesis of 3′ Thioribonucleosides and Their Incorporation into Oligoribonucleotides via Phosphoramidite Chemistry.  RNA. 1997 Nov;3(11):1352-63.

Curley, J. F., Joyce, C. M. and Piccirilli, J. A. Functional Evidence that the 3′-5′ Exonuclease of E. Coli DNA Polymerase Employs a Metal Ion in Leaving Group Stabilization. J. Amer. Chem. Soc., 51:12691-12692 (1997).


Sun, S., Tang, X.-Q., Merchant, A., Anjaneyulu, P. S. R. and Piccirilli, J. A. Efficient Synthesis of 5-(Thioalkyl)uridines via Ring-Opening of alpha-Ureidomethylene Thiolactones. J. Organic Chem., 61:5708-5709 (1996).